Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4UXX

Structure of delta4-DgkA with AMPPCP in 9.9 MAG

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0001727	molecular_function	lipid kinase activity
A	0004143	molecular_function	ATP-dependent diacylglycerol kinase activity
A	0005524	molecular_function	ATP binding
A	0005886	cellular_component	plasma membrane
A	0006629	biological_process	lipid metabolic process
A	0006654	biological_process	phosphatidic acid biosynthetic process
A	0008610	biological_process	lipid biosynthetic process
A	0008654	biological_process	phospholipid biosynthetic process
A	0009411	biological_process	response to UV
A	0016020	cellular_component	membrane
A	0016301	molecular_function	kinase activity
A	0016740	molecular_function	transferase activity
A	0042802	molecular_function	identical protein binding
A	0046872	molecular_function	metal ion binding
B	0000166	molecular_function	nucleotide binding
B	0001727	molecular_function	lipid kinase activity
B	0004143	molecular_function	ATP-dependent diacylglycerol kinase activity
B	0005524	molecular_function	ATP binding
B	0005886	cellular_component	plasma membrane
B	0006629	biological_process	lipid metabolic process
B	0006654	biological_process	phosphatidic acid biosynthetic process
B	0008610	biological_process	lipid biosynthetic process
B	0008654	biological_process	phospholipid biosynthetic process
B	0009411	biological_process	response to UV
B	0016020	cellular_component	membrane
B	0016301	molecular_function	kinase activity
B	0016740	molecular_function	transferase activity
B	0042802	molecular_function	identical protein binding
B	0046872	molecular_function	metal ion binding
C	0000166	molecular_function	nucleotide binding
C	0001727	molecular_function	lipid kinase activity
C	0004143	molecular_function	ATP-dependent diacylglycerol kinase activity
C	0005524	molecular_function	ATP binding
C	0005886	cellular_component	plasma membrane
C	0006629	biological_process	lipid metabolic process
C	0006654	biological_process	phosphatidic acid biosynthetic process
C	0008610	biological_process	lipid biosynthetic process
C	0008654	biological_process	phospholipid biosynthetic process
C	0009411	biological_process	response to UV
C	0016020	cellular_component	membrane
C	0016301	molecular_function	kinase activity
C	0016740	molecular_function	transferase activity
C	0042802	molecular_function	identical protein binding
C	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ZN C 1121

Chain	Residue
C	GLU28
C	GLU76
C	ACP1123

site_id	AC2
Number of Residues	2
Details	BINDING SITE FOR RESIDUE ZN C 1122

Chain	Residue
C	GLU76
C	ACP1123

site_id	AC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE CL A 1121

Chain	Residue
A	ASN27
A	ALA29
A	ARG32

site_id	AC4
Number of Residues	17
Details	BINDING SITE FOR RESIDUE ACP C 1123

Chain	Residue
B	TYR16
B	HOH2001
C	GLU28
C	ASN72
C	GLU76
C	GLU85
C	TYR86
C	HIS87
C	SER90
C	GLY91
C	LYS94
C	ASP95
C	ZN1121
C	ZN1122
C	OLC1125
C	HOH2004
B	ARG9

site_id	AC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MPD B 1122

Chain	Residue
A	ARG81
B	GLU88
B	LEU89
B	SER90
B	ARG92

site_id	AC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE NA A 1122

Chain	Residue
A	GLU28
A	GLU76
A	ACT1123

site_id	AC7
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ACT A 1123

Chain	Residue
A	GLU28
A	GLU76
A	NA1122

site_id	AC8
Number of Residues	7
Details	BINDING SITE FOR RESIDUE OLC C 1124

Chain	Residue
B	ARG9
B	ILE10
C	ALA30
C	GLN33
C	GLU34
C	CYS113
C	OLC1125

site_id	AC9
Number of Residues	10
Details	BINDING SITE FOR RESIDUE OLC B 1123

Chain	Residue
A	SER17
A	CYS113
A	TRP117
B	GLU34
B	ALA37
B	ILE44
B	GLU69
B	ASN72
B	LEU102
B	OLC1124

site_id	BC1
Number of Residues	7
Details	BINDING SITE FOR RESIDUE OLC B 1124

Chain	Residue
A	ILE10
A	TRP117
B	GLN33
B	GLU34
B	TRP112
B	TRP117
B	OLC1123

site_id	BC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE OLC A 1124

Chain	Residue
A	TRP18
A	TRP25
A	ILE26

site_id	BC3
Number of Residues	12
Details	BINDING SITE FOR RESIDUE OLC A 1125

Chain	Residue
A	GLN33
A	GLU34
A	ALA37
A	ILE44
A	VAL62
A	ALA108
A	VAL109
A	TRP112
A	LEU116
B	LEU39
B	LEU40
B	TRP47

site_id	BC4
Number of Residues	10
Details	BINDING SITE FOR RESIDUE OLC C 1125

Chain	Residue
B	ALA13
B	SER17
C	GLU69
C	ASN72
C	SER98
C	LEU102
C	ILE106
C	VAL109
C	ACP1123
C	OLC1124

site_id	BC5
Number of Residues	8
Details	BINDING SITE FOR RESIDUE ACT B 1125

Chain	Residue
B	GLU76
B	GLY83
B	SER84
B	GLU85
B	TYR86
B	HIS87
B	LYS94
B	NA1126

site_id	BC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE NA B 1126

Chain	Residue
B	GLU28
B	GLU76
B	ACT1125

site_id	BC7
Number of Residues	2
Details	BINDING SITE FOR RESIDUE NA C 1126

Chain	Residue
C	GLU88
C	GLU88

site_id	BC8
Number of Residues	1
Details	BINDING SITE FOR RESIDUE ACT A 1126

Chain	Residue
A	HIS119

Functional Information from PROSITE/UniProt

site_id	PS01069
Number of Residues	12
Details	DAGK_PROKAR Prokaryotic diacylglycerol kinase signature. ElLNSAIEavVD

Chain	Residue	Details
A	GLU69-ASP80

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	99
Details	Transmembrane: {"description":"Helical","evidences":[{"source":"PubMed","id":"12379131","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"8071224","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	6
Details	Topological domain: {"description":"Periplasmic","evidences":[{"source":"PubMed","id":"12379131","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"8071224","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	75
Details	Topological domain: {"description":"Cytoplasmic","evidences":[{"source":"PubMed","id":"8071224","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	69
Details	Transmembrane: {"description":"Helical","evidences":[{"source":"PubMed","id":"8071224","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	4
Details	Topological domain: {"description":"Periplasmic","evidences":[{"source":"PubMed","id":"15919996","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8071224","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	3
Details	Active site: {"description":"Proton acceptor","evidences":[{"source":"PubMed","id":"26673816","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"PubMed","id":"25012698","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26673816","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26894538","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	10
Details	Binding site: {"evidences":[{"source":"PubMed","id":"23676677","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"25012698","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26894538","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26960129","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	18
Details	Binding site: {"evidences":[{"source":"PubMed","id":"26673816","evidenceCode":"ECO:0000305"},{"source":"Reference","evidenceCode":"ECO:0000305","citation":{"citationType":"submission","publicationDate":"DEC-2013","submissionDatabase":"PDB data bank","title":"Crystal structure of the integral membrane diacylglycerol kinase with Zn-Amppcp bound and its catalytic mechanism.","authors":["Li D.","Caffrey M."]}}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	9
Details	Binding site: {"evidences":[{"source":"PubMed","id":"23676677","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"25012698","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"25055873","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26673816","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26960129","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	12
Details	Binding site: {"evidences":[{"source":"PubMed","id":"23676677","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"25012698","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"25055873","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26673816","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26894538","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26960129","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	9
Details	Binding site: {"evidences":[{"source":"PubMed","id":"23676677","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"25012698","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26673816","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26894538","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26960129","evidenceCode":"ECO:0000305"},{"source":"Reference","evidenceCode":"ECO:0000305","citation":{"citationType":"submission","publicationDate":"JUN-2013","submissionDatabase":"PDB data bank","title":"Crystal structure of an integral membrane enzyme determined by X-ray free electron laser femtocrystallography.","authors":["Li D.","Howe N.","Caffrey M."]}}]}

Chain

Residue

Details

site_id	SWS_FT_FI13
Number of Residues	3
Details	Binding site: {"evidences":[{"source":"PubMed","id":"23676677","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"25012698","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"25055873","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26673816","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26894538","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26960129","evidenceCode":"ECO:0000305"},{"source":"Reference","evidenceCode":"ECO:0000305","citation":{"citationType":"submission","publicationDate":"JUN-2013","submissionDatabase":"PDB data bank","title":"Crystal structure of an integral membrane enzyme determined by X-ray free electron laser femtocrystallography.","authors":["Li D.","Howe N.","Caffrey M."]}}]}

Chain

Residue

Details

site_id	SWS_FT_FI14
Number of Residues	3
Details	Binding site: {"evidences":[{"source":"PubMed","id":"25012698","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26673816","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26894538","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26960129","evidenceCode":"ECO:0000305"},{"source":"Reference","evidenceCode":"ECO:0000305","citation":{"citationType":"submission","publicationDate":"DEC-2013","submissionDatabase":"PDB data bank","title":"Crystal structure of the integral membrane diacylglycerol kinase with Zn-Amppcp bound and its catalytic mechanism.","authors":["Li D.","Caffrey M."]}}]}

Chain

Residue

Details

site_id	SWS_FT_FI15
Number of Residues	3
Details	Binding site: {"evidences":[{"source":"PubMed","id":"23676677","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"25012698","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26673816","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26894538","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26960129","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI16
Number of Residues	15
Details	Binding site: {"evidences":[{"source":"PubMed","id":"23676677","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"25012698","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"25055873","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26673816","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26894538","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26960129","evidenceCode":"ECO:0000305"},{"source":"Reference","evidenceCode":"ECO:0000305","citation":{"citationType":"submission","publicationDate":"DEC-2013","submissionDatabase":"PDB data bank","title":"Crystal structure of the integral membrane diacylglycerol kinase with Zn-Amppcp bound and its catalytic mechanism.","authors":["Li D.","Caffrey M."]}}]}

Chain

Residue

Details

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)